Chemosensory detection of polyamine metabolites guides C. elegans to nutritive microbes

Much is known about molecular mechanisms by which animals detect pathogenic microbes, but how animals sense beneficial microbes remains poorly understood. The roundworm Caenorhabditis elegans is a microbivore that must distinguish nutritive microbes from pathogens. We characterized a neural circuit used by C. elegans to rapidly discriminate between nutritive bacteria and pathogens. Distinct sensory neuron populations responded to chemical cues from nutritive Escherichia coli and pathogenic Enterococcus faecalis, and these neural signals are decoded by downstream AIB interneurons. The polyamine metabolites cadaverine, putrescine, and spermidine produced by E. coli activate this neural circuit and elicit positive chemotaxis. Our study shows how polyamine odorants can be sensed by animals as proxies for microbe identity and suggests that, hence, polyamines might have widespread roles brokering host-microbe interactions.

Data set includes: instantaneous and end-point lawn occupancy data plotted in Figures 1A-B, a maximum projection image of a volume acquired from the C. elegans strain used for calcium imaging of chemosensory neurons shown in Figure 1C, and spreadsheets containing background corrected calcium measurements shown in Figures 1D-K.
These and all other spreadsheets containing imaging data (.xlsx files) follow the same format.Data are background subtracted fluorescence values extracted from a labeled ROI corresponding to the cell indicated in the file name.Each row is a trial, each column is a frame.Each trial is organized such that it contains 30 seconds prior to the transition described in the file name and 30 seconds following that transition.Data set includes: source data for enrichment of polyamine species in wild-type vs.polyaminesynthesis-deficient E. coli plotted in Figure 6A and source data for measurements of chemotaxis behavior plotted in Figure 6B.

Figure S3 Data
Data set includes: measurements of CaMPARI signals plotted in Figure S3A and a spreadsheet containing source data for calcium measurements plotted in Figure S3B.

Figure S4 Data
Data set includes: source data for behavioral measurements plotted in Figures S4B-C.

Figure S5 Data
Data set includes source data for measurements of the effect of optogenetic inhibition of AIBs on speed plotted in Figure S5.

Figure S6 Data
Data set includes source data for the volcano plot shown in Figure S6.

Figure S9 Data
Data set includes source data for measurements of chemotaxis behavior plotted in Figure S9.

Figure S7 .
Fig. S1.Responses of C. elegans chemosensory neurons to microbe-conditioned media.(A-C) Z-scored calcium signals in AWB, ADF, and ADL neurons in response to switches between E. faecalis-conditioned and E. coli-conditioned media.Data are plotted from 95 trials of AWBs, 96 trials of ADLs, and 56 trials of ASJs.(D) Table categorizing tuning of recorded neurons to E. coli and E. faecalis.In A-C traces of the mean Z-scored signals are shown above heat maps showing the Z-scored signals from individual trials.
Fig. S9.Polyamines increase attraction to E. faecalis.Chemotaxis indices computed from behavioral responses of C. elegans to E. faecalis-conditioned media (n=35 trials), polyamine odorants (n=33 trials), or polyamine odorants added to E. faecalis-conditioned media (n = 36 trials).Each trial used 20 animals.Student's t-test was used to compute the indicated P value.Error bars represent mean plus or minus standard deviation.Each point represents one trial.

Data S2. Source data for Figure 2
Data set includes: A maximum projection image of CaMPARI fluorescence in the head of a C. elegans strain used for CaMPARI experiments shown in Figure2B, source data for CaMPARI measurements plotted in Figure2C, Excel spreadsheets containing background corrected calcium measurements shown in Figures2D-F, source data for chemotaxis measurements shown in Figures2H-I, and source data for effect of AIB silencing on locomotion shown in Figure2K.Data S3.Source data for Figure 3Data set includes: source data for the PCA and volcano plots shown in Figures3A-B, source data for m/z plots shown in Figures C-E, source data for plots showing retention profiles of dansylated polyamines shown in Figure 3F, and source data for enrichment of polyamine species shown in Figure 3G.Data S4.Source data for Figure 4 Data set includes: source data for plot of CaMPARI signals shown in Figure 4A and source data for enrichment of cadaverine in media conditioned by different microbes shown in Figure 4B.Data S5.Source data for Figure 5 Data set includes: Spreadsheets (.xlsx files) containing source data for plots of calcium signals in sensory neurons shown in Figures 5A-H, and measurements of chemotaxis behavior plotted in Figure 5I.Data S6.Source data for Figure 6

Figure S1 Data
Figure S1 DataData set includes source data for plots of calcium signaling in sensory neurons shown in FigureS1A-C.

Figure S2 Data
Figure S2 Data Data set includes source data for plots of calcium signaling in sensory neurons shown in Figure S2A-B.

Figure S7 Data
Figure S7 Data Data set includes source data for plots of calcium signaling in sensory neurons shown in Figure S7A-B.

Figure S8 Data
Figure S8 Data Data set includes source data for heatmaps of calcium signaling in sensory neurons shown in Figure S8A-B.

2 Table S1 . Metabolites differentially expressed by E. coli and E. faecalis.
This table contains data regarding Fig.3.Metabolite identity is determined as noted in Methods, above.Enrichment values across each of the three replicates for E. coli-conditioned media, E. faecalis-conditioned media, and Luria Broth (unconditioned media) are shown.Table is included in a separate file due to size.

Table S2 . Targeted polyamine profiling of a panel of microbes.
This table contains data regarding Figs.3 and 4. Metabolite identity is determined as noted in Methods, above.Enrichment values are shown for all replicates of each microbe.9 replicates were performed for E. coli-conditioned media, E. faecalis-conditioned media, and Luria Broth and 3 replicates were performed for all other samples.Highlighted values indicate undetected values that were replaced with the detection threshold.Table is included in a separate file due to size.

Table S3 . Strains used in this study
This table contains a list of the strains of C. elegans that were used in this study, as well as their origins.

Table S4 .
Genotyping primersThis table contains information on the oligonucleotide primers used to verify genotypes of relevant C. elegans strains.

Table S5 .
Plasmids for transgenesisThis table contains information on the plasmids used to generate some of the transgenic C. elegans strains used.
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